Variant report

Variant	rs16969547
Chromosome Location	chr15:39964889-39964890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:39913171..39923947-chr15:39954798..39966806,32	MCF-7	breast:
2	chr15:39960868..39962395-chr15:39964357..39966165,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10083552	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10152903	1.00[CHB][hapmap]
rs10152951	1.00[CHB][hapmap]
rs1051442	1.00[CHB][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10520141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10520143	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10520145	0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10520146	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520147	1.00[CHB][hapmap]
rs10520148	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520149	0.81[YRI][hapmap]
rs10520152	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1073675	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs12324669	0.81[YRI][hapmap]
rs12324682	1.00[JPT][hapmap]
rs1382443	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs1382444	1.00[CHB][hapmap]
rs16969167	1.00[CHB][hapmap]
rs16969335	1.00[JPT][hapmap]
rs16969338	1.00[JPT][hapmap]
rs16969352	1.00[JPT][hapmap]
rs16969484	0.86[ASN][1000 genomes]
rs16969487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16969491	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16969573	0.86[ASN][1000 genomes]
rs16969662	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969663	1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969664	1.00[CHB][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes]
rs16969666	1.00[CHB][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes]
rs16969672	1.00[CHB][hapmap];0.93[YRI][hapmap]
rs16969678	0.86[ASN][1000 genomes]
rs16969679	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs16969680	1.00[CHB][hapmap];0.88[YRI][hapmap]
rs16969688	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs16969692	0.92[ASW][hapmap];0.82[LWK][hapmap];0.88[YRI][hapmap]
rs16969701	0.88[YRI][hapmap]
rs16969702	0.92[YRI][hapmap]
rs16969718	0.81[YRI][hapmap]
rs16969723	0.81[YRI][hapmap]
rs16969724	0.81[YRI][hapmap]
rs17632916	0.82[EUR][1000 genomes]
rs17633107	1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs17633210	1.00[CHB][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs17705806	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs17706083	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17706179	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs17717859	1.00[CHB][hapmap]
rs1813493	0.80[EUR][1000 genomes]
rs1994380	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2129455	0.81[YRI][hapmap]
rs2129457	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171309	0.81[YRI][hapmap]
rs2228262	1.00[CHB][hapmap]
rs2228263	1.00[CHB][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs2411316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2618156	0.80[EUR][1000 genomes]
rs2618161	1.00[CHB][hapmap]
rs2618164	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2618165	1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2618167	1.00[CHB][hapmap]
rs2664136	0.81[EUR][1000 genomes]
rs2664137	0.80[EUR][1000 genomes]
rs2664138	1.00[CHB][hapmap]
rs28377784	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28549326	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28619289	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28625134	0.84[AFR][1000 genomes]
rs28653011	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28735552	1.00[ASN][1000 genomes]
rs28785006	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs34878675	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4085744	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41315060	0.82[EUR][1000 genomes]
rs4322636	0.86[ASN][1000 genomes]
rs4415979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4503768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45461294	0.84[EUR][1000 genomes]
rs4923835	1.00[CHB][hapmap]
rs55899942	0.80[AFR][1000 genomes]
rs56862147	0.82[AFR][1000 genomes]
rs58188999	0.85[EUR][1000 genomes]
rs58878379	0.82[AFR][1000 genomes]
rs59146042	0.86[ASN][1000 genomes]
rs59578395	0.85[EUR][1000 genomes]
rs59628570	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs60228643	1.00[ASN][1000 genomes]
rs6492905	1.00[CHB][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs7171057	0.81[YRI][hapmap]
rs7172155	1.00[CHB][hapmap];0.81[YRI][hapmap]
rs7172346	0.81[YRI][hapmap]
rs7173948	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs7179604	1.00[CHB][hapmap]
rs7180740	0.88[YRI][hapmap]
rs7181354	1.00[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs7182423	1.00[CHB][hapmap];0.88[YRI][hapmap];0.80[AFR][1000 genomes]
rs7183462	0.92[ASW][hapmap];0.93[LWK][hapmap];0.81[YRI][hapmap]
rs72727029	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72727060	0.80[AFR][1000 genomes]
rs74008647	0.85[EUR][1000 genomes]
rs74008648	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8036035	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8041266	1.00[CHB][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes]
rs880270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs937961	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[LWK][hapmap];0.88[YRI][hapmap]
rs937962	1.00[CHB][hapmap];0.87[YRI][hapmap]
rs954152	0.81[EUR][1000 genomes]
rs9972350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16969547	CASC5	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39960200-39972600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr15:39964600-39972600	Weak transcription	HSMMtube	muscle
3	chr15:39964600-39974000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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